Streamlining Quantitative Analysis of Long RNA Sequencing Reads
Transcriptome analyses allow for linking RNA expression profiles to cellular pathways and phenotypes. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads. Currently, available data analysis software often l...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-10-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/21/19/7259 |
| _version_ | 1797552009664004096 |
|---|---|
| author | Sebastian Oeck Alicia I. Tüns Sebastian Hurst Alexander Schramm |
| author_facet | Sebastian Oeck Alicia I. Tüns Sebastian Hurst Alexander Schramm |
| author_sort | Sebastian Oeck |
| collection | DOAJ |
| description | Transcriptome analyses allow for linking RNA expression profiles to cellular pathways and phenotypes. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads. Currently, available data analysis software often lacks cost- and time-efficient workflows. Although kit-based workflows and benchtop platforms for RNA sequencing provide software options, e.g., cloud-based tools to analyze basecalled reads, quantitative, and easy-to-use solutions for transcriptome analysis, especially for non-human data, are missing. We therefore developed a user-friendly tool, termed Alignator, for rapid analysis of long RNA reads requiring only FASTQ files and an Ensembl cDNA database reference. After successful mapping, Alignator generates quantitative information for each transcript and provides a table in which sequenced and aligned RNA are stored for further comparative analyses. |
| first_indexed | 2024-03-10T15:54:01Z |
| format | Article |
| id | doaj.art-853238f5dfd9445eb53df7917cc45657 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:54:01Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-853238f5dfd9445eb53df7917cc456572023-11-20T15:47:28ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012119725910.3390/ijms21197259Streamlining Quantitative Analysis of Long RNA Sequencing ReadsSebastian Oeck0Alicia I. Tüns1Sebastian Hurst2Alexander Schramm3Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, GermanyDepartment of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, GermanyInstitute of Cell Biology, University of Münster, 48149 Münster, GermanyDepartment of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, GermanyTranscriptome analyses allow for linking RNA expression profiles to cellular pathways and phenotypes. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads. Currently, available data analysis software often lacks cost- and time-efficient workflows. Although kit-based workflows and benchtop platforms for RNA sequencing provide software options, e.g., cloud-based tools to analyze basecalled reads, quantitative, and easy-to-use solutions for transcriptome analysis, especially for non-human data, are missing. We therefore developed a user-friendly tool, termed Alignator, for rapid analysis of long RNA reads requiring only FASTQ files and an Ensembl cDNA database reference. After successful mapping, Alignator generates quantitative information for each transcript and provides a table in which sequenced and aligned RNA are stored for further comparative analyses.https://www.mdpi.com/1422-0067/21/19/7259Alignatorlong readsalignmentRNAFASTQsequencing tool |
| spellingShingle | Sebastian Oeck Alicia I. Tüns Sebastian Hurst Alexander Schramm Streamlining Quantitative Analysis of Long RNA Sequencing Reads International Journal of Molecular Sciences Alignator long reads alignment RNA FASTQ sequencing tool |
| title | Streamlining Quantitative Analysis of Long RNA Sequencing Reads |
| title_full | Streamlining Quantitative Analysis of Long RNA Sequencing Reads |
| title_fullStr | Streamlining Quantitative Analysis of Long RNA Sequencing Reads |
| title_full_unstemmed | Streamlining Quantitative Analysis of Long RNA Sequencing Reads |
| title_short | Streamlining Quantitative Analysis of Long RNA Sequencing Reads |
| title_sort | streamlining quantitative analysis of long rna sequencing reads |
| topic | Alignator long reads alignment RNA FASTQ sequencing tool |
| url | https://www.mdpi.com/1422-0067/21/19/7259 |
| work_keys_str_mv | AT sebastianoeck streamliningquantitativeanalysisoflongrnasequencingreads AT aliciaituns streamliningquantitativeanalysisoflongrnasequencingreads AT sebastianhurst streamliningquantitativeanalysisoflongrnasequencingreads AT alexanderschramm streamliningquantitativeanalysisoflongrnasequencingreads |